Thank you so much David W. If you don't mind could you please kindly give me a example of biopython script to blast a set of genome sequences against themselves? A tutorial script will be very helpful for me. Another is what will be the command line in python if i want to save the output file as .csv format from your aforementioned script? David, sorry for long reply but please kindly look at the following problem, actually this is the main problem which i try to fragmented and want to solve.
Problem: A homologous gene group consists of genes, which have an alignment to at least one other gene in the group with both a % sequence coverage and % identity equal to or higher than a given stringency cutoff. Write a python program to find the number of homologous gene groups within a genome at various levels of stringency. For example with a stringency of 10, every gene in a group should have a % sequence coverage and % identity of at least 10% with at least one other gene in the group. The program should take a single genome file in genbank format on the command line and write a csv file called "output.csv" in the directory. The ouput file should consist of 10 lines, each line should have the stringency used (0 to 100, in increments of 10) and the number of homology groups. (See example below). Submit the python program as a txt file.
[0,13456] [10,234] [20,234] [30,200] [40,190] [50,187] [60,187] [70,100] [80,95 ] [90,55] [100,45]
"Stringency cutoff was defined by % of coverage in the gene alignment and % sequence identity"
I have full permission to help from peer, mentor, bioinformatics forum and sites. I need your valuable suggestions regarding this problem.
I remember that you asked similar question earlier. Could you please provide some examples input file ?
I am in a serious problem regarding this python script. Don't get solution yet and this is why I am asking repeatedly for help in this forum. Input file should be a single genome file in genbank format like NC_011000.gbk ftp://ftp.ncbi.nlm.nih.gov/genomes/Bacteria/Burkholderia_cenocepacia_J2315_uid57953/ I am a beginner in programing language. I try to solve this problem by reading biopython tutorial , cookbook. unfortunately I did not write the script yet.
Why you want to start task from .gbk files ? Why not .fasta files ? Just wanna reconfirm that you were saying about BLASTN ?